CSLAP<-read.csv("CSLAP_Dataset_09232019.csv", header=TRUE)
CSLAP$Sample_Year<-as.factor(CSLAP$Sample_Year)
CSLAP$Sample_Month<-as.factor(CSLAP$Sample_Month)
#Split by `Info_Type`
OWCSLAP<-CSLAP[CSLAP$Info_Type == "OW",]
BSCSLAP<-CSLAP[CSLAP$Info_Type == "BS",]
SBCSLAP<-CSLAP[CSLAP$Info_Type == "SB",]
noSBCSLAP<-CSLAP[CSLAP$Info_Type != "SB",]
redCSLAP<-read.csv("redCSLAP.csv")
redOWCSLAP<-redCSLAP[redCSLAP$Info_Type == "OW",]
redBSCSLAP<-redCSLAP[redCSLAP$Info_Type == "BS",]
redSBCSLAP<-redCSLAP[redCSLAP$Info_Type == "SB",]
rednoSBCSLAP<-redCSLAP[redCSLAP$Info_Type != "SB",]
LakeID and Sample_Year#Select out data of interest
df <- OWCSLAP %>% dplyr::select(TP_mg.L, Dreissenids, CA.SA, Mean_Depth_m, Sample_Year, Sample_Month, LakeID)
df <- df[complete.cases(df), ]
#Remove lakes and year 2015
df <- df[df$LakeID != "0601GUI0188",]
df <- df[df$LakeID != "1201ECA0697", ]
df <- df[df$LakeID != "1701LLO0708", ]
df <- df[df$LakeID != "1201GAL0563", ]
df <- df[df$Sample_Year != "2015",]
df$LakeID <- as.factor(as.character(df$LakeID))
OWTP<-glm(TP_mg.L+1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=df, family=Gamma(link="identity"))
summary(OWTP)
##
## Call:
## glm(formula = TP_mg.L + 1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m),
## family = Gamma(link = "identity"), data = df)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -0.010728 -0.003571 -0.001395 0.001973 0.061486
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 1.0164616 0.0005768 1762.377 < 2e-16 ***
## DreissenidsUninvaded -0.0022936 0.0003926 -5.842 5.95e-09 ***
## log(CA.SA) 0.0002040 0.0001271 1.605 0.109
## log(Mean_Depth_m) -0.0023559 0.0002034 -11.585 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 3.55969e-05)
##
## Null deviance: 0.079669 on 2113 degrees of freedom
## Residual deviance: 0.074080 on 2110 degrees of freedom
## AIC: -15632
##
## Number of Fisher Scoring iterations: 3
plot(OWTP)
qqPlot(resid(OWTP))
## 3989 123
## 1714 58
simOWTP <- simulateResiduals(OWTP)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simOWTP)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
BSTP<-glm(TP_mg.L+1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=BSCSLAP, family=Gamma(link="identity"))
summary(BSTP)
##
## Call:
## glm(formula = TP_mg.L + 1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m),
## family = Gamma(link = "identity"), data = BSCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -0.07956 -0.04778 -0.02916 -0.00214 2.01241
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 1.058383 0.016518 64.076 < 2e-16 ***
## DreissenidsUninvaded 0.020215 0.009781 2.067 0.0389 *
## log(CA.SA) 0.015291 0.003504 4.364 1.35e-05 ***
## log(Mean_Depth_m) -0.031107 0.007766 -4.006 6.43e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 0.02022613)
##
## Null deviance: 22.032 on 1846 degrees of freedom
## Residual deviance: 21.421 on 1843 degrees of freedom
## (104 observations deleted due to missingness)
## AIC: -2807.5
##
## Number of Fisher Scoring iterations: 5
plot(BSTP)
qqPlot(resid(BSTP))
## 20 31
## 10 16
simBSTP <- simulateResiduals(BSTP)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simBSTP)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
OWTN<-glm(TN_mg.L+1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=OWCSLAP, family=Gamma(link="identity"))
summary(OWTN)
##
## Call:
## glm(formula = TN_mg.L + 1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m),
## family = Gamma(link = "identity"), data = OWCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -0.3947 -0.1060 -0.0449 0.0285 3.7172
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 1.549277 0.037903 40.875 < 2e-16 ***
## DreissenidsUninvaded -0.142040 0.027153 -5.231 1.82e-07 ***
## log(CA.SA) 0.019655 0.007835 2.509 0.012182 *
## log(Mean_Depth_m) -0.043181 0.012570 -3.435 0.000601 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 0.08901886)
##
## Null deviance: 104.31 on 2684 degrees of freedom
## Residual deviance: 100.16 on 2681 degrees of freedom
## (67 observations deleted due to missingness)
## AIC: 517.16
##
## Number of Fisher Scoring iterations: 6
plot(OWTN)
qqPlot(resid(OWTN))
## 4237 271
## 2294 141
simOWTN <- simulateResiduals(OWTN)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simOWTN)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
OWChl<-glm(Extracted_Chl.a_ug.L+.01 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=OWCSLAP, family=Gamma(link="identity"))
summary(OWChl)
##
## Call:
## glm(formula = Extracted_Chl.a_ug.L + 0.01 ~ Dreissenids + log(CA.SA) +
## log(Mean_Depth_m), family = Gamma(link = "identity"), data = OWCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.6840 -0.7151 -0.3112 0.1963 4.5504
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 3.92702 0.25152 15.613 < 2e-16 ***
## DreissenidsUninvaded 0.71415 0.15490 4.610 4.21e-06 ***
## log(CA.SA) 0.15724 0.05482 2.868 0.00416 **
## log(Mean_Depth_m) -1.02768 0.10569 -9.724 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 1.013149)
##
## Null deviance: 1938.2 on 2636 degrees of freedom
## Residual deviance: 1827.7 on 2633 degrees of freedom
## (115 observations deleted due to missingness)
## AIC: 11139
##
## Number of Fisher Scoring iterations: 8
plot(OWChl)
qqPlot(resid(OWChl))
## 60 1644
## 29 810
simOWChl <- simulateResiduals(OWChl)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simOWChl)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
OWSecchi<-glm(Secchi_Depth_m ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=OWCSLAP, family=Gamma(link="identity"))
summary(OWSecchi)
##
## Call:
## glm(formula = Secchi_Depth_m ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m),
## family = Gamma(link = "identity"), data = OWCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.24637 -0.27292 -0.04745 0.18312 1.33146
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 3.21666 0.11972 26.867 < 2e-16 ***
## DreissenidsUninvaded -0.29053 0.09374 -3.099 0.00196 **
## log(CA.SA) -0.26453 0.02623 -10.085 < 2e-16 ***
## log(Mean_Depth_m) 1.09994 0.02847 38.640 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 0.1186655)
##
## Null deviance: 427.44 on 2632 degrees of freedom
## Residual deviance: 312.56 on 2629 degrees of freedom
## (119 observations deleted due to missingness)
## AIC: 8959.9
##
## Number of Fisher Scoring iterations: 6
plot(OWSecchi)
qqPlot(resid(OWSecchi))
## 4432 368
## 2359 171
simOWSecchi <- simulateResiduals(OWSecchi)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simOWSecchi)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
OWTC<-glm(True_Color_PTU ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=OWCSLAP, family=Gamma(link="identity"))
summary(OWTC)
##
## Call:
## glm(formula = True_Color_PTU ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m),
## family = Gamma(link = "identity"), data = OWCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.2571 -0.5533 -0.1622 0.2630 2.2626
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 15.1038 0.8208 18.401 < 2e-16 ***
## DreissenidsUninvaded 2.0558 0.5100 4.031 5.71e-05 ***
## log(CA.SA) 1.8840 0.1784 10.562 < 2e-16 ***
## log(Mean_Depth_m) -3.6529 0.3203 -11.404 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 0.4162008)
##
## Null deviance: 1179.3 on 2655 degrees of freedom
## Residual deviance: 1064.0 on 2652 degrees of freedom
## (96 observations deleted due to missingness)
## AIC: 18653
##
## Number of Fisher Scoring iterations: 12
plot(OWTC)
qqPlot(resid(OWTC))
## 1174 3254
## 571 1729
simOWTC <- simulateResiduals(OWTC)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simOWTC)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
SBChl<-glm(ESF_Chl.a_ug.L+1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=SBCSLAP, family=Gamma(link="identity"))
## Warning: glm.fit: algorithm did not converge
summary(SBChl)
##
## Call:
## glm(formula = ESF_Chl.a_ug.L + 1 ~ Dreissenids + log(CA.SA) +
## log(Mean_Depth_m), family = Gamma(link = "identity"), data = SBCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -3.6258 -2.4781 -1.8809 -0.7808 6.3404
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 4526.0 2591.3 1.747 0.0821 .
## DreissenidsUninvaded 500.3 924.5 0.541 0.5889
## log(CA.SA) 635.3 755.8 0.841 0.4015
## log(Mean_Depth_m) -2210.1 1152.2 -1.918 0.0564 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 11.10688)
##
## Null deviance: 1163.9 on 223 degrees of freedom
## Residual deviance: 1140.7 on 220 degrees of freedom
## (2 observations deleted due to missingness)
## AIC: 3518.4
##
## Number of Fisher Scoring iterations: 25
plot(SBChl)
qqPlot(resid(SBChl))
## 1115 1089
## 73 63
simSBChl <- simulateResiduals(SBChl)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simSBChl)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
SBmicro<-glm(ESF_Microcystin_ug.L+1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=SBCSLAP, family=Gamma(link="identity"))
## Warning in log(ifelse(y == 0, 1, y/mu)): NaNs produced
## Warning: step size truncated due to divergence
## Warning in log(ifelse(y == 0, 1, y/mu)): NaNs produced
## Warning in log(ifelse(y == 0, 1, y/mu)): NaNs produced
## Warning in log(ifelse(y == 0, 1, y/mu)): NaNs produced
## Warning in log(ifelse(y == 0, 1, y/mu)): NaNs produced
## Warning in log(ifelse(y == 0, 1, y/mu)): NaNs produced
## Warning in log(ifelse(y == 0, 1, y/mu)): NaNs produced
## Warning in log(ifelse(y == 0, 1, y/mu)): NaNs produced
## Warning in log(ifelse(y == 0, 1, y/mu)): NaNs produced
## Warning: glm.fit: algorithm did not converge
summary(SBmicro)
##
## Call:
## glm(formula = ESF_Microcystin_ug.L + 1 ~ Dreissenids + log(CA.SA) +
## log(Mean_Depth_m), family = Gamma(link = "identity"), data = SBCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -3.5620 -2.0461 -1.1396 0.0506 4.5952
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 2143 1240 1.728 0.0914 .
## DreissenidsUninvaded 3093 1611 1.919 0.0617 .
## log(CA.SA) -2630 1391 -1.890 0.0656 .
## log(Mean_Depth_m) 1575 1030 1.529 0.1337
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 5.364112)
##
## Null deviance: 259.73 on 45 degrees of freedom
## Residual deviance: 161.20 on 42 degrees of freedom
## (180 observations deleted due to missingness)
## AIC: 614.36
##
## Number of Fisher Scoring iterations: 25
plot(SBmicro)
qqPlot(resid(SBmicro))
## 1100 629
## 32 15
simSBmicro <- simulateResiduals(SBmicro)
plotSimulatedResiduals(simSBmicro)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
OWTP2<-glm(TP_mg.L+1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=df, family=Gamma(link="log"))
summary(OWTP2)
##
## Call:
## glm(formula = TP_mg.L + 1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m),
## family = Gamma(link = "log"), data = df)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -0.010727 -0.003570 -0.001394 0.001973 0.061488
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.0163358 0.0005701 28.653 < 2e-16 ***
## DreissenidsUninvaded -0.0022666 0.0003878 -5.845 5.86e-09 ***
## log(CA.SA) 0.0002013 0.0001258 1.601 0.11
## log(Mean_Depth_m) -0.0023277 0.0002009 -11.585 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 3.55984e-05)
##
## Null deviance: 0.079669 on 2113 degrees of freedom
## Residual deviance: 0.074083 on 2110 degrees of freedom
## AIC: -15631
##
## Number of Fisher Scoring iterations: 3
plot(OWTP2)
qqPlot(resid(OWTP2))
## 3989 123
## 1714 58
simOWTP2 <- simulateResiduals(OWTP2)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simOWTP2)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
BSTP2<-glm(TP_mg.L+1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=BSCSLAP, family=Gamma(link="log"))
summary(BSTP2)
##
## Call:
## glm(formula = TP_mg.L + 1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m),
## family = Gamma(link = "log"), data = BSCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -0.08022 -0.04780 -0.02898 -0.00191 2.01106
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.056030 0.015708 3.567 0.00037 ***
## DreissenidsUninvaded 0.019628 0.009378 2.093 0.03649 *
## log(CA.SA) 0.014847 0.003336 4.451 9.05e-06 ***
## log(Mean_Depth_m) -0.029833 0.007365 -4.050 5.32e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 0.02019946)
##
## Null deviance: 22.032 on 1846 degrees of freedom
## Residual deviance: 21.411 on 1843 degrees of freedom
## (104 observations deleted due to missingness)
## AIC: -2808.4
##
## Number of Fisher Scoring iterations: 4
plot(BSTP2)
qqPlot(resid(BSTP2))
## 20 31
## 10 16
simBSTP2 <- simulateResiduals(BSTP2)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simBSTP2)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
OWTN2<-glm(TN_mg.L+1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=OWCSLAP, family=Gamma(link="log"))
summary(OWTN2)
##
## Call:
## glm(formula = TN_mg.L + 1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m),
## family = Gamma(link = "log"), data = OWCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -0.3962 -0.1056 -0.0448 0.0284 3.7210
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.435499 0.026146 16.657 < 2e-16 ***
## DreissenidsUninvaded -0.098875 0.018091 -5.465 5.05e-08 ***
## log(CA.SA) 0.015820 0.005609 2.821 0.004828 **
## log(Mean_Depth_m) -0.030536 0.008914 -3.426 0.000622 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 0.0890692)
##
## Null deviance: 104.31 on 2684 degrees of freedom
## Residual deviance: 100.06 on 2681 degrees of freedom
## (67 observations deleted due to missingness)
## AIC: 514.5
##
## Number of Fisher Scoring iterations: 4
plot(OWTN2)
qqPlot(resid(OWTN2))
## 4237 271
## 2294 141
simOWTN2 <- simulateResiduals(OWTN2)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simOWTN2)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
OWChl2<-glm(Extracted_Chl.a_ug.L+.01 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=OWCSLAP, family=Gamma(link="log"))
summary(OWChl2)
##
## Call:
## glm(formula = Extracted_Chl.a_ug.L + 0.01 ~ Dreissenids + log(CA.SA) +
## log(Mean_Depth_m), family = Gamma(link = "log"), data = OWCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.7084 -0.7178 -0.3104 0.1996 4.5537
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 1.20915 0.08989 13.451 < 2e-16 ***
## DreissenidsUninvaded 0.27980 0.06159 4.543 5.8e-06 ***
## log(CA.SA) 0.05457 0.01925 2.835 0.00462 **
## log(Mean_Depth_m) -0.26078 0.03038 -8.583 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 1.010626)
##
## Null deviance: 1938.2 on 2636 degrees of freedom
## Residual deviance: 1835.2 on 2633 degrees of freedom
## (115 observations deleted due to missingness)
## AIC: 11151
##
## Number of Fisher Scoring iterations: 5
plot(OWChl2)
qqPlot(resid(OWChl2))
## 60 1644
## 29 810
simOWChl2 <- simulateResiduals(OWChl2)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simOWChl2)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
OWSecchi2<-glm(Secchi_Depth_m ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=OWCSLAP, family=Gamma(link="log"))
summary(OWSecchi2)
##
## Call:
## glm(formula = Secchi_Depth_m ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m),
## family = Gamma(link = "log"), data = OWCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.2639 -0.2661 -0.0516 0.1866 1.3115
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 1.149878 0.030371 37.861 < 2e-16 ***
## DreissenidsUninvaded -0.077716 0.020945 -3.711 0.000211 ***
## log(CA.SA) -0.086146 0.006593 -13.066 < 2e-16 ***
## log(Mean_Depth_m) 0.318868 0.010555 30.211 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 0.1188637)
##
## Null deviance: 427.44 on 2632 degrees of freedom
## Residual deviance: 311.91 on 2629 degrees of freedom
## (119 observations deleted due to missingness)
## AIC: 8954.3
##
## Number of Fisher Scoring iterations: 4
plot(OWSecchi2)
qqPlot(resid(OWSecchi2))
## 4432 368
## 2359 171
simOWSecchi2 <- simulateResiduals(OWSecchi2)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simOWSecchi2)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
OWTC2<-glm(True_Color_PTU ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=OWCSLAP, family=Gamma(link="log"))
summary(OWTC2)
##
## Call:
## glm(formula = True_Color_PTU ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m),
## family = Gamma(link = "log"), data = OWCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.2588 -0.5467 -0.1512 0.2657 2.2738
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 2.63403 0.05677 46.401 < 2e-16 ***
## DreissenidsUninvaded 0.15040 0.03920 3.837 0.000128 ***
## log(CA.SA) 0.13774 0.01219 11.296 < 2e-16 ***
## log(Mean_Depth_m) -0.23044 0.01927 -11.959 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 0.4126261)
##
## Null deviance: 1179.3 on 2655 degrees of freedom
## Residual deviance: 1057.2 on 2652 degrees of freedom
## (96 observations deleted due to missingness)
## AIC: 18635
##
## Number of Fisher Scoring iterations: 7
plot(OWTC2)
qqPlot(resid(OWTC2))
## 1174 1323
## 571 647
simOWTC2 <- simulateResiduals(OWTC2)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simOWTC2)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
SBChl2<-glm(ESF_Chl.a_ug.L+1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=SBCSLAP, family=Gamma(link="log"))
## Warning: glm.fit: algorithm did not converge
summary(SBChl2)
##
## Call:
## glm(formula = ESF_Chl.a_ug.L + 1 ~ Dreissenids + log(CA.SA) +
## log(Mean_Depth_m), family = Gamma(link = "log"), data = SBCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -3.5090 -2.5512 -1.8732 -0.7115 6.5521
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 9.11707 0.94182 9.680 < 2e-16 ***
## DreissenidsUninvaded 0.09243 0.48142 0.192 0.84793
## log(CA.SA) 0.13311 0.29358 0.453 0.65072
## log(Mean_Depth_m) -1.05893 0.38415 -2.757 0.00633 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 9.766356)
##
## Null deviance: 1163.9 on 223 degrees of freedom
## Residual deviance: 1137.1 on 220 degrees of freedom
## (2 observations deleted due to missingness)
## AIC: 3517.4
##
## Number of Fisher Scoring iterations: 25
plot(SBChl2)
qqPlot(resid(SBChl2))
## 1115 1089
## 73 63
simSBChl2 <- simulateResiduals(SBChl2)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simSBChl2)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
SBmicro2<-glm(ESF_Microcystin_ug.L+1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=SBCSLAP, family=Gamma(link="log"))
## Warning: glm.fit: algorithm did not converge
summary(SBmicro2)
##
## Call:
## glm(formula = ESF_Microcystin_ug.L + 1 ~ Dreissenids + log(CA.SA) +
## log(Mean_Depth_m), family = Gamma(link = "log"), data = SBCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -20.713 -13.707 -8.175 -2.534 4.839
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -353.9838 4.6022 -76.92 <2e-16 ***
## DreissenidsUninvaded -134.5380 0.9398 -143.16 <2e-16 ***
## log(CA.SA) 182.1964 1.8263 99.76 <2e-16 ***
## log(Mean_Depth_m) 127.1322 1.6808 75.64 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 5.934985)
##
## Null deviance: 259.73 on 45 degrees of freedom
## Residual deviance: 4945.56 on 42 degrees of freedom
## (180 observations deleted due to missingness)
## AIC: 884.24
##
## Number of Fisher Scoring iterations: 25
plot(SBmicro2)
qqPlot(resid(SBmicro2))
## 1100 1015
## 32 20
simSBmicro2 <- simulateResiduals(SBmicro2)
plotSimulatedResiduals(simSBmicro2)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
OWTP3<-glm(TP_mg.L+1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=df, family=Gamma(link="inverse"))
summary(OWTP3)
##
## Call:
## glm(formula = TP_mg.L + 1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m),
## family = Gamma(link = "inverse"), data = df)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -0.010726 -0.003570 -0.001393 0.001974 0.061490
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.9837887 0.0005636 1745.641 < 2e-16 ***
## DreissenidsUninvaded 0.0022399 0.0003831 5.847 5.78e-09 ***
## log(CA.SA) -0.0001987 0.0001245 -1.597 0.11
## log(Mean_Depth_m) 0.0022999 0.0001985 11.586 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 3.559991e-05)
##
## Null deviance: 0.079669 on 2113 degrees of freedom
## Residual deviance: 0.074086 on 2110 degrees of freedom
## AIC: -15631
##
## Number of Fisher Scoring iterations: 3
plot(OWTP3)
qqPlot(resid(OWTP3))
## 3989 123
## 1714 58
simOWTP3 <- simulateResiduals(OWTP3)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simOWTP3)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
BSTP3<-glm(TP_mg.L+1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=BSCSLAP, family=Gamma(link="inverse"))
summary(BSTP3)
##
## Call:
## glm(formula = TP_mg.L + 1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m),
## family = Gamma(link = "inverse"), data = BSCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -0.08091 -0.04792 -0.02870 -0.00170 2.00964
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.946228 0.014934 63.361 < 2e-16 ***
## DreissenidsUninvaded -0.019071 0.008993 -2.121 0.0341 *
## log(CA.SA) -0.014419 0.003174 -4.543 5.91e-06 ***
## log(Mean_Depth_m) 0.028615 0.006981 4.099 4.33e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 0.02017152)
##
## Null deviance: 22.032 on 1846 degrees of freedom
## Residual deviance: 21.401 on 1843 degrees of freedom
## (104 observations deleted due to missingness)
## AIC: -2809.2
##
## Number of Fisher Scoring iterations: 4
plot(BSTP3)
qqPlot(resid(BSTP3))
## 20 31
## 10 16
simBSTP3 <- simulateResiduals(BSTP3)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simBSTP3)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
OWTN3<-glm(TN_mg.L+1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=OWCSLAP, family=Gamma(link="inverse"))
summary(OWTN3)
##
## Call:
## glm(formula = TN_mg.L + 1 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m),
## family = Gamma(link = "inverse"), data = OWCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -0.3984 -0.1056 -0.0449 0.0290 3.7254
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.649279 0.018026 36.019 < 2e-16 ***
## DreissenidsUninvaded 0.069149 0.012054 5.737 1.07e-08 ***
## log(CA.SA) -0.012774 0.003984 -3.206 0.001362 **
## log(Mean_Depth_m) 0.021516 0.006297 3.417 0.000643 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 0.08911749)
##
## Null deviance: 104.31 on 2684 degrees of freedom
## Residual deviance: 99.93 on 2681 degrees of freedom
## (67 observations deleted due to missingness)
## AIC: 511.07
##
## Number of Fisher Scoring iterations: 5
plot(OWTN3)
qqPlot(resid(OWTN3))
## 4237 271
## 2294 141
simOWTN3 <- simulateResiduals(OWTN3)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simOWTN3)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
OWChl3<-glm(Extracted_Chl.a_ug.L+.01 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=OWCSLAP, family=Gamma(link="inverse"))
summary(OWChl3)
##
## Call:
## glm(formula = Extracted_Chl.a_ug.L + 0.01 ~ Dreissenids + log(CA.SA) +
## log(Mean_Depth_m), family = Gamma(link = "inverse"), data = OWCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.7074 -0.7178 -0.3073 0.1980 4.5255
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.361262 0.031100 11.616 < 2e-16 ***
## DreissenidsUninvaded -0.108103 0.025051 -4.315 1.65e-05 ***
## log(CA.SA) -0.018969 0.005897 -3.217 0.00131 **
## log(Mean_Depth_m) 0.058955 0.007364 8.006 1.76e-15 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 1.007162)
##
## Null deviance: 1938.2 on 2636 degrees of freedom
## Residual deviance: 1843.5 on 2633 degrees of freedom
## (115 observations deleted due to missingness)
## AIC: 11164
##
## Number of Fisher Scoring iterations: 7
plot(OWChl3)
qqPlot(resid(OWChl3))
## 60 1644
## 29 810
simOWChl3 <- simulateResiduals(OWChl3)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simOWChl3)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
OWSecchi3<-glm(Secchi_Depth_m ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=OWCSLAP, family=Gamma(link="inverse"))
summary(OWSecchi3)
##
## Call:
## glm(formula = Secchi_Depth_m ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m),
## family = Gamma(link = "inverse"), data = OWCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.26170 -0.27334 -0.05502 0.18845 1.32723
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.307871 0.007093 43.402 < 2e-16 ***
## DreissenidsUninvaded 0.020455 0.004645 4.404 1.11e-05 ***
## log(CA.SA) 0.022983 0.001510 15.222 < 2e-16 ***
## log(Mean_Depth_m) -0.078289 0.002811 -27.854 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 0.1203673)
##
## Null deviance: 427.44 on 2632 degrees of freedom
## Residual deviance: 315.20 on 2629 degrees of freedom
## (119 observations deleted due to missingness)
## AIC: 8982.5
##
## Number of Fisher Scoring iterations: 5
plot(OWSecchi3)
qqPlot(resid(OWSecchi3))
## 4432 368
## 2359 171
simOWSecchi3 <- simulateResiduals(OWSecchi3)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simOWSecchi3)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
OWTC3<-glm(True_Color_PTU ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=OWCSLAP, family=Gamma(link="inverse"))
summary(OWTC3)
##
## Call:
## glm(formula = True_Color_PTU ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m),
## family = Gamma(link = "inverse"), data = OWCSLAP)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.2644 -0.5599 -0.1380 0.2560 2.2384
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.0782548 0.0038001 20.593 < 2e-16 ***
## DreissenidsUninvaded -0.0108886 0.0029502 -3.691 0.000228 ***
## log(CA.SA) -0.0094469 0.0007224 -13.077 < 2e-16 ***
## log(Mean_Depth_m) 0.0129348 0.0009760 13.253 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for Gamma family taken to be 0.4099815)
##
## Null deviance: 1179.3 on 2655 degrees of freedom
## Residual deviance: 1052.3 on 2652 degrees of freedom
## (96 observations deleted due to missingness)
## AIC: 18622
##
## Number of Fisher Scoring iterations: 6
plot(OWTC3)
qqPlot(resid(OWTC3))
## 1174 1323
## 571 647
simOWTC3 <- simulateResiduals(OWTC3)
## Model family was recognized or set as continuous, but duplicate values were detected in the response. Consider if you are fitting an appropriate model.
plotSimulatedResiduals(simOWTC3)
## plotSimulatedResiduals is deprecated, switch your code to using the plot function
`Model won’t run
SBChl3<-glm(ESF_Chl.a_ug.L+.01 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=SBCSLAP, family=Gamma(link="inverse"))
summary(SBChl3)
plot(SBChl3)
qqPlot(resid(SBChl3))
simSBChl3 <- simulateResiduals(SBChl3)
plotSimulatedResiduals(simSBChl3)
`Model won’t run
SBmicro3<-glm(ESF_Microcystin_ug.L+.01 ~ Dreissenids + log(CA.SA) + log(Mean_Depth_m), data=SBCSLAP, family=Gamma(link="inverse"))
summary(SBmicro3)
plot(SBmicro3)
qqPlot(resid(SBmicro3))
simSBmicro3 <- simulateResiduals(SBmicro3)
plotSimulatedResiduals(simSBmicro3)
plot(OWTP)
plot(OWTP2)
plot(OWTP3)
plot(BSTP)
plot(BSTP2)
plot(BSTP3)
plot(OWTN)
plot(OWTN2)
plot(OWTN3)
plot(OWChl)
plot(OWChl2)
plot(OWChl3)
plot(OWSecchi)
plot(OWSecchi2)
plot(OWSecchi3)
plot(OWTC)
plot(OWTC2)
plot(OWTC3)
-NOTE Gamma(“inverse”) did not work
plot(SBChl)
plot(SBChl2)
-NOTE Gamma(“inverse”) did not work
plot(SBmicro)
plot(SBmicro2)